Hi Skyline Team,
I am trying to import mass spectrometry result using SkylineDailyRunner.
A brief description of the procedure:
- Have created a template, template.sky (attached below)
- I open that file and import a transition list (attached below)
- Then I import results, there are 143 of those. Each named SHRSP_xxx.d where xxx varies from 001 to 143. (have attached a .zip containing SHRSP_001.d)
- Export the report using a custom PythonTemplate.skyr (attached below)
I am able to do this flawlessly using the Skyline Daily GUI, and a correct report is generated as expected. However, when I try to replicate the procedure by creating a .bat file for SkylineDailyRunner, it throws the error mentioned below. I have attached the .bat file as well.
Code for the bat file
C:/MSIC_Master/SkylineDailyRunner.exe --in=C:/MSIC_Master/template.sky --import-process-count=4 --import-transition-list=C:\MSIC_Master\Data\Ruwan_SHRSP_MPfeatures_13_TL.csv --import-all-files=C:\MSIC_Master\Data --report-name=PythonTemplate --report-file=C:\MSIC_Master\Data\Ruwan_SHRSP_MPfeatures_13.tsv --report-format=TSV --out=C:\MSIC_Master\Data\Ruwan_SHRSP_MPfeatures_13.sky
It throws a similar error for all 143 files.
Error: Failed importing the results file SHRSP_001.d.
Message: System.IO.IOException: Error: Failed importing the results file C:\MSIC_Master\Data\SHRSP_001.d.
Message: pwiz.Skyline.Model.Results.MissingDataException: No scans in C:\MSIC_Master\Data\SHRSP_001.d match the current filter settings. ---> pwiz.Skyline.Model.Results.NoFullScanDataException: No scans in C:\MSIC_Master\Data\SHRSP_001.d match the current filter settings.
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 362
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 215
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList`1 chromatogramRequestOrder) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 548
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 403
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263
--- End of inner exception stack trace ---
at pwiz.Skyline.Model.Results.ChromatogramCache.RunProcess(ProcessStartInfo psi, String importProgressPipe, IProgressStatus status, ILoadMonitor loader) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 683
at pwiz.Skyline.Model.Results.ChromatogramCache.Run(MsDataFileUri msDataFileUri, String documentFilePath, String cachePath, IProgressStatus status, ILoadMonitor loader) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 644
at pwiz.Skyline.Model.Results.ChromatogramCache.Build(SrmDocument document, String documentFilePath, ChromatogramCache cacheRecalc, String cachePath, MsDataFileUri msDataFileUri, IProgressStatus status, ILoadMonitor loader, Action`2 complete) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 607
Would be really thankful if someone could provide a possible solution/ cause of error.
Regards
Veerupaksh